package main;

import io.PermutationReader;

import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.util.NoSuchElementException;

import org.biojava.bio.BioException;

import utils.Driver;
import utils.Database;
import utils.Permutator;

public class Main {
	private final static String permFile = "permutations6_new";

	public static void main(String[] args) throws NoSuchElementException,
			BioException, IOException {
		Database db = new Database("sequences/LSURef93_lbl.fasta");
		System.out.println("Number of LSU organisms: " + db.getOrganisms().size());
		Permutator p = new Permutator(6, "sequences/" + permFile);

		Driver d = new Driver(db, new FileInputStream(new File("sequences/"
				+ permFile)), "sequences/outputaa.csv");

		System.out.println("Program finished");
	}
}
